Define a genetic component trait

Creates one row in trait_meta describing a genetic component trait: a quantity with QTL effects in genome_effects, genetic values in ind_tgv, and additive genetic variance in trait_var_comp. Contains no phenotype-level information.

To register the observed phenotype that individuals receive records for, call define_phenotype() after this function.

The trait's genetic targets are not set here. Store them with define_effect_cov_matrix() (effect_name = "additive"), or pass G to define_additive_effects(), which writes the target together with the effects calibrated to it. The usual chain is define_trait() → define_additive_effects(G = ) → define_phenotype().

Usage

define_trait(
  pop,
  trait_name,
  description = NULL,
  units = NULL,
  overwrite = FALSE
)

Arguments

pop

A tidybreed_pop object.

trait_name

Character. Unique identifier for this genetic component trait. Must be a valid SQL identifier.

description

Character. Free-text description of the trait.

units

Character. Measurement units, e.g. "kg", "count".

overwrite

Logical. If TRUE and a trait with the same name already exists, replace its trait_meta row and clear associated phenotype_effects rows. Default FALSE errors if the trait already exists.

Value

The modified tidybreed_pop (invisibly).

See also

define_phenotype(), define_additive_effects(), define_effect_fixed_class(), define_effect_fixed_cov(), define_effect_random(), add_phenotype(), define_effect_cov_matrix()

Examples

if (FALSE) { # \dontrun{
# Simple genetic component trait, its target and its effects:
pop <- pop |>
  define_trait("ADG", units = "g/day")
pop <- get_table(pop, "genome_meta") |>
  define_additive_effects("ADG", G = 100)

# Maternal component traits (no define_phenotype call needed for WWD/WWM):
pop <- pop |>
  define_trait("WWD") |>
  define_trait("WWM")
pop <- get_table(pop, "genome_meta") |>
  define_additive_effects(c("WWD", "WWM"),
    G = matrix(c(200, -40, -40, 80), 2, 2))

# Then define the observed composite phenotype:
pop <- pop |>
  define_phenotype("WW", type = "continuous", mean = 230,
    residual_var = 180,
    components = tibble::tribble(
      ~source_trait_name, ~contributor_type,
      "WWD", "self",
      "WWM", "dam"
    ))
} # }